** RETRANSMISSION TO CORRECT DATE ** Capt. John Cota, center, leaves a federal courthouse in San Francisco, Friday, March 6, 2009, with his wife, Teresa Barrett, right, and attorney Claudia Quiroz, left, after he plea guilty to misdemeanor charges. Cota was the pilot at the helm of the cargo ship Cosco Busan that caused a massive oil spill in the San Francisco in Nov. 2007. (AP Photo/Paul Sakuma)

Photo: Paul Sakuma, AP

** RETRANSMISSION TO CORRECT DATE ** Capt. John Cota, center,...

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In this April, 4, 2008 file photo, Capt. John Cota is shown outside the Federal Building in San Francisco. Cota who was piloting the Cosco Busan when it struck a bridge support spilling 53,000 gallons of oil into the San Francisco Bay has decided to retire rather than testify in an upcoming legal proceeding.

Photo: Jeff Chiu, AP

In this April, 4, 2008 file photo, Capt. John Cota is shown outside...

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Cosco Busan sits south of the Bay Bridge two days after it had struck a Bay Bridge tower near Yerba Buena Island on Wednsday, Nov. 7, 2007 spilling 58,000 gallons of fuel into San Francisco Bay. Jakub Mosur / The Chronicle

The pilot of the container ship that struck the Bay Bridge in 2007 and spilled 53,000 gallons of fuel oil pleaded guilty Friday to federal water pollution charges in an agreement that calls for him to serve two to 10 months in prison.

Capt. John Cota, 61, admitted in a San Francisco courtroom that he acted negligently in piloting the 901-foot-long Cosco Busan in a heavy morning fog Nov. 7, 2007, without using the ship's radar or discussing his plans with the captain and crew. He also admitted failing to disclose all the prescription drugs he was taking when he renewed his federal and state pilot's licenses in 2006 and 2007.

But his negotiated plea agreement nearly fell apart when a prosecutor read a lengthy account of Cota's alleged misdeeds and his lawyer protested that it was full of inaccuracies.

Illston reproached Assistant U.S. Attorney Jonathan Schmidt for "arguing for the grandstand." After Schmidt backed off and accepted Cota's account in the plea agreement of his own shortcomings, Illston allowed Cota to plead guilty to misdemeanor charges of violating the Clean Water Act and the Migratory Bird Act. She scheduled sentencing for June 19.

Besides imprisonment, the plea agreement includes a fine of between $3,000 and $30,000. Cota, a vessel pilot for 26 years, has surrendered his license and said in his plea agreement that he would not reapply until January 2010.

Cota and the ship's owners and operators are also defendants in civil damage suits by state and federal agencies and by fishers and crabbers seeking reimbursement for their losses.

The guilty plea "is a reminder that the Cosco Busan crash was not just an accident, but a criminal act," Justice Department official John Cruden said in a statement. "This is not a case involving a mere mistake."

Bornstein told reporters that the government is "trying to make Capt. Cota out to be a scapegoat" for an accident that had multiple causes.

Prosecutors agreed to dismiss felony charges that Cota lied in annual physical exams about the medications he was taking. Cota admitted in the plea agreement that he omitted some medications from the forms he provided to state and federal licensing authorities, including a sleep-disorder drug, but did not say he had knowingly lied.

The Cosco Busan hit the second tower of the bridge west of Yerba Buena Island. Oil pouring from a gash on the ship's port side killed more than 2,000 birds and reached the bay shoreline and ocean beaches in Marin and San Mateo counties. Government agencies have estimated the cost of the damage and the cleanup at $60 million.

The board also faulted the ship's captain for failing to plot a navigation plan or communicate with Cota. It criticized state and federal regulators for continuing to license Cota despite his sleep disorder, his use of medications known to affect judgment, and what investigators described as his history of accidents.

The ship's operating company, Fleet Management Ltd. of Hong Kong, still faces six felony charges for allegedly falsifying documents to interfere with the federal investigation. Illston granted the company's request to postpone its trial from April to Sept. 14.